<?xml version="1.0" encoding="ascii"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
          "DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
  <title>BIP.Bayes.PlotMeld</title>
  <link rel="stylesheet" href="epydoc.css" type="text/css" />
  <script type="text/javascript" src="epydoc.js"></script>
</head>

<body bgcolor="white" text="black" link="blue" vlink="#204080"
      alink="#204080">
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
       bgcolor="#a0c0ff" cellspacing="0">
  <tr valign="middle">
  <!-- Home link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="BIP-module.html">Home</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Tree link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Index link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Help link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Project homepage -->
      <th class="navbar" align="right" width="100%">
        <table border="0" cellpadding="0" cellspacing="0">
          <tr><th class="navbar" align="center"
            ><a class="navbar" target="_top" href="http://code.google.com/p/bayesian-inference">Project Homepage</a></th>
          </tr></table></th>
  </tr>
</table>
<table width="100%" cellpadding="0" cellspacing="0">
  <tr valign="top">
    <td width="100%">
      <span class="breadcrumbs">
        <a href="BIP-module.html">Package&nbsp;BIP</a> ::
        <a href="BIP.Bayes-module.html">Package&nbsp;Bayes</a> ::
        Module&nbsp;PlotMeld
      </span>
    </td>
    <td>
      <table cellpadding="0" cellspacing="0">
        <!-- hide/show private -->
        <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
    onclick="toggle_private();">hide&nbsp;private</a>]</span></td></tr>
        <tr><td align="right"><span class="options"
            >[<a href="frames.html" target="_top">frames</a
            >]&nbsp;|&nbsp;<a href="BIP.Bayes.PlotMeld-pysrc.html"
            target="_top">no&nbsp;frames</a>]</span></td></tr>
      </table>
    </td>
  </tr>
</table>
<h1 class="epydoc">Source Code for <a href="BIP.Bayes.PlotMeld-module.html">Module BIP.Bayes.PlotMeld</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-comment"># To change this template, choose Tools | Templates</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-comment"># and open the template in the editor.</tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"><tt class="py-docstring">Module with specialized plotting functions for the Melding results</tt> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-name">__author__</tt><tt class="py-op">=</tt><tt class="py-string">"fccoelho"</tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt class="py-name">__date__</tt> <tt class="py-op">=</tt><tt class="py-string">"$06/01/2010 11:24:20$"</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"><tt class="py-name">__docformat__</tt> <tt class="py-op">=</tt> <tt class="py-string">"restructuredtext en"</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">itertools</tt> <tt class="py-keyword">import</tt> <tt class="py-name">cycle</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">scipy</tt> <tt class="py-keyword">import</tt> <tt class="py-name">stats</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">glob</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">numpy</tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">matplotlib</tt><tt class="py-op">.</tt><tt class="py-name">pyplot</tt> <tt class="py-keyword">as</tt> <tt class="py-name">P</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">scipy</tt><tt class="py-op">.</tt><tt class="py-name">stats</tt> <tt class="py-keyword">import</tt> <tt class="py-name">gaussian_kde</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line"> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"> </tt>
<a name="plot_series"></a><div id="plot_series-def"><a name="L19"></a><tt class="py-lineno"> 19</tt> <a class="py-toggle" href="#" id="plot_series-toggle" onclick="return toggle('plot_series');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.PlotMeld-module.html#plot_series">plot_series</a><tt class="py-op">(</tt><tt class="py-param">tim</tt><tt class="py-op">,</tt><tt class="py-param">series</tt><tt class="py-op">,</tt><tt class="py-param">y</tt><tt class="py-op">,</tt> <tt class="py-param">names</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-param">title</tt><tt class="py-op">=</tt><tt class="py-string">'series'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="plot_series-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="plot_series-expanded"><a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line">    <tt class="py-name">c</tt> <tt class="py-op">=</tt> <tt class="py-name">cycle</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'b'</tt><tt class="py-op">,</tt><tt class="py-string">'g'</tt><tt class="py-op">,</tt><tt class="py-string">'r'</tt><tt class="py-op">,</tt><tt class="py-string">'c'</tt><tt class="py-op">,</tt><tt class="py-string">'m'</tt><tt class="py-op">,</tt><tt class="py-string">'y'</tt><tt class="py-op">,</tt><tt class="py-string">'k'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">names</tt><tt class="py-op">:</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line">        <tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">series</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line">    <tt class="py-comment">#l = len(names)</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt><tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line">        <tt class="py-comment">#print n</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line">        <tt class="py-comment">#P.subplot(l,1,i)</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line">        <tt class="py-name">co</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">next</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line">        <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">scoreatpercentile</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt><tt class="py-number">5</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">series</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">co</tt><tt class="py-op">+</tt><tt class="py-string">'-.'</tt><tt class="py-op">)</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line">        <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">scoreatpercentile</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt><tt class="py-number">95</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">series</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">co</tt><tt class="py-op">+</tt><tt class="py-string">'-.'</tt><tt class="py-op">)</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line">        <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">scoreatpercentile</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt><tt class="py-number">50</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">series</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">co</tt><tt class="py-op">+</tt><tt class="py-string">'-'</tt><tt class="py-op">,</tt><tt class="py-name">lw</tt><tt class="py-op">=</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-name">label</tt><tt class="py-op">=</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line">        <tt class="py-comment">#P.plot(tim,y[:,list(series.dtype.names).index(n)],'*',label=n+' obs.')</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">y</tt><tt class="py-op">:</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line">            <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-string">'*'</tt><tt class="py-op">,</tt><tt class="py-name">label</tt><tt class="py-op">=</tt><tt class="py-name">n</tt><tt class="py-op">+</tt><tt class="py-string">' obs.'</tt><tt class="py-op">)</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">savefig</tt><tt class="py-op">(</tt><tt class="py-name">title</tt><tt class="py-op">+</tt><tt class="py-string">'.png'</tt><tt class="py-op">)</tt> </tt>
</div><a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line"> </tt>
<a name="plot_pred"></a><div id="plot_pred-def"><a name="L36"></a><tt class="py-lineno"> 36</tt> <a class="py-toggle" href="#" id="plot_pred-toggle" onclick="return toggle('plot_pred');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.PlotMeld-module.html#plot_pred">plot_pred</a><tt class="py-op">(</tt><tt class="py-param">tim</tt><tt class="py-op">,</tt><tt class="py-param">series</tt><tt class="py-op">,</tt><tt class="py-param">y</tt><tt class="py-op">,</tt> <tt class="py-param">fig</tt><tt class="py-op">,</tt><tt class="py-param">names</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-param">title</tt><tt class="py-op">=</tt><tt class="py-string">'series'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="plot_pred-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="plot_pred-expanded"><a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line">    <tt class="py-name">c</tt> <tt class="py-op">=</tt> <tt class="py-name">cycle</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'b'</tt><tt class="py-op">,</tt><tt class="py-string">'g'</tt><tt class="py-op">,</tt><tt class="py-string">'r'</tt><tt class="py-op">,</tt><tt class="py-string">'c'</tt><tt class="py-op">,</tt><tt class="py-string">'m'</tt><tt class="py-op">,</tt><tt class="py-string">'y'</tt><tt class="py-op">,</tt><tt class="py-string">'k'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">names</tt><tt class="py-op">:</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line">        <tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">series</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line">    <tt class="py-name">l</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">names</tt><tt class="py-op">)</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line">    <tt class="py-name">ax</tt> <tt class="py-op">=</tt> <tt class="py-name">fig</tt><tt class="py-op">.</tt><tt class="py-name">add_subplot</tt><tt class="py-op">(</tt><tt class="py-number">111</tt><tt class="py-op">)</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt><tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line">        <tt class="py-name">co</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">next</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">b</tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-number">2.5</tt><tt class="py-op">,</tt><tt class="py-number">25</tt><tt class="py-op">,</tt><tt class="py-number">50</tt><tt class="py-op">,</tt><tt class="py-number">75</tt><tt class="py-op">,</tt><tt class="py-number">97.5</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">b</tt> <tt class="py-op">==</tt> <tt class="py-number">50</tt><tt class="py-op">:</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line">                <tt class="py-name">st</tt> <tt class="py-op">=</tt> <tt class="py-string">'k-'</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line">                <tt class="py-name">st</tt> <tt class="py-op">=</tt> <tt class="py-string">'%s:'</tt><tt class="py-op">%</tt><tt class="py-name">co</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line">            <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line">                <tt class="py-name">lower</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">scoreatpercentile</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">+</tt><tt class="py-name">b</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">series</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">]</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line">                <tt class="py-name">upper</tt> <tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">scoreatpercentile</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt><tt class="py-number">100</tt><tt class="py-op">-</tt><tt class="py-name">b</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">series</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">]</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line">                <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">,</tt><tt class="py-name">lower</tt><tt class="py-op">,</tt><tt class="py-name">st</tt><tt class="py-op">,</tt><tt class="py-name">tim</tt><tt class="py-op">,</tt><tt class="py-name">upper</tt><tt class="py-op">,</tt><tt class="py-name">st</tt><tt class="py-op">,</tt><tt class="py-name">label</tt><tt class="py-op">=</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line">                <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">fill_between</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">,</tt><tt class="py-name">lower</tt><tt class="py-op">,</tt><tt class="py-name">upper</tt><tt class="py-op">,</tt><tt class="py-name">facecolor</tt><tt class="py-op">=</tt><tt class="py-name">co</tt><tt class="py-op">,</tt><tt class="py-name">alpha</tt><tt class="py-op">=</tt><tt class="py-number">0.12</tt><tt class="py-op">)</tt><tt class="py-comment">#</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line">            <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line">                <tt class="py-keyword">pass</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">y</tt><tt class="py-op">:</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line">            <tt class="py-comment">#print y[n].shape, tim.shape</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line">            <tt class="py-keyword">try</tt><tt class="py-op">:</tt> <tt class="py-comment">#in the last window we run out of date points</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line">                <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-string">'^'</tt><tt class="py-op">,</tt><tt class="py-name">label</tt><tt class="py-op">=</tt><tt class="py-name">n</tt><tt class="py-op">+</tt><tt class="py-string">' obs.'</tt><tt class="py-op">)</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line">            <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line">                <tt class="py-keyword">pass</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">savefig</tt><tt class="py-op">(</tt><tt class="py-name">title</tt><tt class="py-op">+</tt><tt class="py-string">'.png'</tt><tt class="py-op">)</tt> </tt>
</div><a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line"> </tt>
<a name="pred_new_cases"></a><div id="pred_new_cases-def"><a name="L64"></a><tt class="py-lineno"> 64</tt> <a class="py-toggle" href="#" id="pred_new_cases-toggle" onclick="return toggle('pred_new_cases');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.PlotMeld-module.html#pred_new_cases">pred_new_cases</a><tt class="py-op">(</tt><tt class="py-param">obs</tt><tt class="py-op">,</tt><tt class="py-param">series</tt><tt class="py-op">,</tt><tt class="py-param">weeks</tt><tt class="py-op">,</tt><tt class="py-param">fig</tt><tt class="py-op">,</tt> <tt class="py-param">names</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-param">ws</tt><tt class="py-op">=</tt><tt class="py-number">7</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="pred_new_cases-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="pred_new_cases-expanded"><a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line"><tt class="py-docstring">    Predicted total new cases in a week vs oserved.</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line">    <tt class="py-name">fig</tt> <tt class="py-op">=</tt><tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">figure</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">title</tt><tt class="py-op">(</tt><tt class="py-string">'Total new cases per week: predicted vs observed'</tt><tt class="py-op">)</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">names</tt><tt class="py-op">:</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line">        <tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">series</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line">    <tt class="py-name">ax</tt> <tt class="py-op">=</tt> <tt class="py-name">fig</tt><tt class="py-op">.</tt><tt class="py-name">add_subplot</tt><tt class="py-op">(</tt><tt class="py-number">111</tt><tt class="py-op">)</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line"> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">names</tt><tt class="py-op">:</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line">        <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">boxplot</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">s</tt> <tt class="py-keyword">in</tt> <tt class="py-name">series</tt><tt class="py-op">]</tt> <tt class="py-op">,</tt><tt class="py-name">positions</tt> <tt class="py-op">=</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">weeks</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">notch</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">vert</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line">        <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">weeks</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">s</tt> <tt class="py-keyword">in</tt> <tt class="py-name">series</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-string">'^'</tt><tt class="py-op">,</tt> <tt class="py-name">label</tt><tt class="py-op">=</tt><tt class="py-string">"Mean pred. %s"</tt><tt class="py-op">%</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line">        <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">weeks</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">obs</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">ws</tt><tt class="py-op">:</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">ws</tt><tt class="py-op">+</tt><tt class="py-name">ws</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">w</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">weeks</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-string">'r-o'</tt><tt class="py-op">,</tt> <tt class="py-name">label</tt><tt class="py-op">=</tt><tt class="py-string">"obs. Prev"</tt><tt class="py-op">)</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">xlabel</tt><tt class="py-op">(</tt><tt class="py-string">'weeks'</tt><tt class="py-op">)</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">legend</tt><tt class="py-op">(</tt><tt class="py-name">loc</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
</div><a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line"> </tt>
<a name="plot_series2"></a><div id="plot_series2-def"><a name="L81"></a><tt class="py-lineno"> 81</tt> <a class="py-toggle" href="#" id="plot_series2-toggle" onclick="return toggle('plot_series2');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.PlotMeld-module.html#plot_series2">plot_series2</a><tt class="py-op">(</tt><tt class="py-param">tim</tt><tt class="py-op">,</tt><tt class="py-param">obs</tt><tt class="py-op">,</tt><tt class="py-param">series</tt><tt class="py-op">,</tt><tt class="py-param">names</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-param">tit</tt><tt class="py-op">=</tt><tt class="py-string">'Simulated vs Observed series'</tt><tt class="py-op">,</tt><tt class="py-param">ws</tt><tt class="py-op">=</tt><tt class="py-number">7</tt><tt class="py-op">,</tt><tt class="py-param">lag</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="plot_series2-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="plot_series2-expanded"><a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line">    <tt class="py-name">ser2</tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">series</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">:</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line">        <tt class="py-name">ser2</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">concatenate</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">s</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">s</tt> <tt class="py-keyword">in</tt> <tt class="py-name">series</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line">    <tt class="py-comment">#print type (series)#.I.shape</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">    <tt class="py-name">fig</tt> <tt class="py-op">=</tt><tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">figure</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">title</tt><tt class="py-op">(</tt><tt class="py-name">tit</tt><tt class="py-op">)</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">names</tt><tt class="py-op">:</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line">        <tt class="py-name">names</tt> <tt class="py-op">=</tt> <tt class="py-name">ser2</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line">    <tt class="py-name">ax</tt> <tt class="py-op">=</tt> <tt class="py-name">fig</tt><tt class="py-op">.</tt><tt class="py-name">add_subplot</tt><tt class="py-op">(</tt><tt class="py-number">111</tt><tt class="py-op">)</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line">    <tt class="py-name">c</tt> <tt class="py-op">=</tt> <tt class="py-name">cycle</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'b'</tt><tt class="py-op">,</tt><tt class="py-string">'g'</tt><tt class="py-op">,</tt><tt class="py-string">'r'</tt><tt class="py-op">,</tt><tt class="py-string">'c'</tt><tt class="py-op">,</tt><tt class="py-string">'m'</tt><tt class="py-op">,</tt><tt class="py-string">'y'</tt><tt class="py-op">,</tt><tt class="py-string">'k'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line">    <tt class="py-keyword">print</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">obs</tt><tt class="py-op">[</tt><tt class="py-string">'I'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">median</tt><tt class="py-op">(</tt><tt class="py-name">ser2</tt><tt class="py-op">[</tt><tt class="py-string">'I'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">names</tt><tt class="py-op">:</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line">        <tt class="py-name">co</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">next</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line">        <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">,</tt><tt class="py-name">obs</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-string">'%s+'</tt><tt class="py-op">%</tt><tt class="py-name">co</tt><tt class="py-op">,</tt> <tt class="py-name">label</tt><tt class="py-op">=</tt><tt class="py-string">"Observed %s"</tt><tt class="py-op">%</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line">        <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-name">ws</tt><tt class="py-op">*</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">lag</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">median</tt><tt class="py-op">(</tt><tt class="py-name">ser2</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-string">'k-'</tt><tt class="py-op">)</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line">        <tt class="py-name">lower</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">scoreatpercentile</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ser2</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">]</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line">        <tt class="py-name">upper</tt> <tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">scoreatpercentile</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt><tt class="py-number">98</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ser2</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">T</tt><tt class="py-op">]</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line">        <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">fill_between</tt><tt class="py-op">(</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">tim</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-name">ws</tt><tt class="py-op">*</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">lag</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">lower</tt><tt class="py-op">,</tt><tt class="py-name">upper</tt><tt class="py-op">,</tt><tt class="py-name">facecolor</tt><tt class="py-op">=</tt><tt class="py-name">co</tt><tt class="py-op">,</tt><tt class="py-name">alpha</tt><tt class="py-op">=</tt><tt class="py-number">0.6</tt><tt class="py-op">)</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">xlabel</tt><tt class="py-op">(</tt><tt class="py-string">'days'</tt><tt class="py-op">)</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line">    <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">legend</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line"> </tt>
<a name="plot_par_series"></a><div id="plot_par_series-def"><a name="L103"></a><tt class="py-lineno">103</tt> <a class="py-toggle" href="#" id="plot_par_series-toggle" onclick="return toggle('plot_par_series');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.PlotMeld-module.html#plot_par_series">plot_par_series</a><tt class="py-op">(</tt><tt class="py-param">tim</tt><tt class="py-op">,</tt><tt class="py-param">ptlist</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="plot_par_series-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="plot_par_series-expanded"><a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">figure</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">title</tt><tt class="py-op">(</tt><tt class="py-string">'Parameters temporal variation'</tt><tt class="py-op">)</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt><tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">ptlist</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line">        <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">subplot</tt><tt class="py-op">(</tt><tt class="py-number">3</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">i</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line">        <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">boxplot</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">s</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">s</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ptlist</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">notch</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">positions</tt><tt class="py-op">=</tt><tt class="py-name">tim</tt><tt class="py-op">,</tt><tt class="py-name">vert</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line">        <tt class="py-comment">#P.errorbar(tim,[median(t[n]) for t in ptlist],yerr=[std(t[n]) for t in ptlist],label=n)</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line">        <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">ylabel</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">xlabel</tt><tt class="py-op">(</tt><tt class="py-string">'Weeks'</tt><tt class="py-op">)</tt> </tt>
</div><a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line"> </tt>
<a name="plot_par_violin"></a><div id="plot_par_violin-def"><a name="L113"></a><tt class="py-lineno">113</tt> <a class="py-toggle" href="#" id="plot_par_violin-toggle" onclick="return toggle('plot_par_violin');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.PlotMeld-module.html#plot_par_violin">plot_par_violin</a><tt class="py-op">(</tt><tt class="py-param">tim</tt><tt class="py-op">,</tt><tt class="py-param">ptlist</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="plot_par_violin-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="plot_par_violin-expanded"><a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line">    <tt class="py-name">fig</tt> <tt class="py-op">=</tt> <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">figure</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">    <tt class="py-comment">#P.title('Parameters temporal variation')</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt><tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">ptlist</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">dtype</tt><tt class="py-op">.</tt><tt class="py-name">names</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line">        <tt class="py-name">ax</tt> <tt class="py-op">=</tt> <tt class="py-name">fig</tt><tt class="py-op">.</tt><tt class="py-name">add_subplot</tt><tt class="py-op">(</tt><tt class="py-number">3</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">i</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">        <tt id="link-0" class="py-name" targets="Function BIP.Bayes.PlotMeld.violin_plot()=BIP.Bayes.PlotMeld-module.html#violin_plot"><a title="BIP.Bayes.PlotMeld.violin_plot" class="py-name" href="#" onclick="return doclink('link-0', 'violin_plot', 'link-0');">violin_plot</a></tt><tt class="py-op">(</tt><tt class="py-name">ax</tt><tt class="py-op">,</tt><tt class="py-op">[</tt><tt class="py-name">s</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">s</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ptlist</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">tim</tt><tt class="py-op">,</tt><tt class="py-name">bp</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line">        <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">ylabel</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">xlabel</tt><tt class="py-op">(</tt><tt class="py-string">'Weeks'</tt><tt class="py-op">)</tt> </tt>
</div><a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line"> </tt>
<a name="violin_plot"></a><div id="violin_plot-def"><a name="L122"></a><tt class="py-lineno">122</tt> <a class="py-toggle" href="#" id="violin_plot-toggle" onclick="return toggle('violin_plot');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BIP.Bayes.PlotMeld-module.html#violin_plot">violin_plot</a><tt class="py-op">(</tt><tt class="py-param">ax</tt><tt class="py-op">,</tt><tt class="py-param">data</tt><tt class="py-op">,</tt><tt class="py-param">positions</tt><tt class="py-op">,</tt><tt class="py-param">bp</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="violin_plot-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="violin_plot-expanded"><a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line">    <tt class="py-docstring">'''</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line"><tt class="py-docstring">    Create violin plots on an axis</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line"><tt class="py-docstring">    '''</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line">    <tt class="py-name">dist</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">positions</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">positions</tt><tt class="py-op">)</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line">    <tt class="py-name">w</tt> <tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-number">0.15</tt><tt class="py-op">*</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">dist</tt><tt class="py-op">,</tt><tt class="py-number">1.0</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-number">0.5</tt><tt class="py-op">)</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">d</tt><tt class="py-op">,</tt><tt class="py-name">p</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt><tt class="py-name">positions</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line">        <tt class="py-name">k</tt> <tt class="py-op">=</tt> <tt class="py-name">gaussian_kde</tt><tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">)</tt> <tt class="py-comment">#calculates the kernel density</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line">        <tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt class="py-name">k</tt><tt class="py-op">.</tt><tt class="py-name">dataset</tt><tt class="py-op">.</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-comment">#lower bound of violin</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line">        <tt id="link-1" class="py-name" targets="Variable BIP.SDE.example.M=BIP.SDE.example-module.html#M"><a title="BIP.SDE.example.M" class="py-name" href="#" onclick="return doclink('link-1', 'M', 'link-1');">M</a></tt> <tt class="py-op">=</tt> <tt class="py-name">k</tt><tt class="py-op">.</tt><tt class="py-name">dataset</tt><tt class="py-op">.</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-comment">#upper bound of violin</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line">        <tt class="py-name">x</tt> <tt class="py-op">=</tt> <tt class="py-name">arange</tt><tt class="py-op">(</tt><tt class="py-name">m</tt><tt class="py-op">,</tt><tt id="link-2" class="py-name"><a title="BIP.SDE.example.M" class="py-name" href="#" onclick="return doclink('link-2', 'M', 'link-1');">M</a></tt><tt class="py-op">,</tt><tt class="py-op">(</tt><tt id="link-3" class="py-name"><a title="BIP.SDE.example.M" class="py-name" href="#" onclick="return doclink('link-3', 'M', 'link-1');">M</a></tt><tt class="py-op">-</tt><tt class="py-name">m</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-number">100.</tt><tt class="py-op">)</tt> <tt class="py-comment"># support for violin</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line">        <tt class="py-name">v</tt> <tt class="py-op">=</tt> <tt class="py-name">k</tt><tt class="py-op">.</tt><tt class="py-name">evaluate</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt> <tt class="py-comment">#violin profile (density curve)</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line">        <tt class="py-name">v</tt> <tt class="py-op">=</tt> <tt class="py-name">v</tt><tt class="py-op">/</tt><tt class="py-name">v</tt><tt class="py-op">.</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">w</tt> <tt class="py-comment">#scaling the violin to the available space</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line">        <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">fill_betweenx</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">p</tt><tt class="py-op">,</tt><tt class="py-name">v</tt><tt class="py-op">+</tt><tt class="py-name">p</tt><tt class="py-op">,</tt><tt class="py-name">facecolor</tt><tt class="py-op">=</tt><tt class="py-string">'y'</tt><tt class="py-op">,</tt><tt class="py-name">alpha</tt><tt class="py-op">=</tt><tt class="py-number">0.3</tt><tt class="py-op">)</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line">        <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">fill_betweenx</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">p</tt><tt class="py-op">,</tt><tt class="py-op">-</tt><tt class="py-name">v</tt><tt class="py-op">+</tt><tt class="py-name">p</tt><tt class="py-op">,</tt><tt class="py-name">facecolor</tt><tt class="py-op">=</tt><tt class="py-string">'y'</tt><tt class="py-op">,</tt><tt class="py-name">alpha</tt><tt class="py-op">=</tt><tt class="py-number">0.3</tt><tt class="py-op">)</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">bp</tt><tt class="py-op">:</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line">        <tt class="py-name">ax</tt><tt class="py-op">.</tt><tt class="py-name">boxplot</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt><tt class="py-name">notch</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">positions</tt><tt class="py-op">=</tt><tt class="py-name">positions</tt><tt class="py-op">,</tt><tt class="py-name">vert</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
</div><a name="L139"></a><tt class="py-lineno">139</tt>  <tt class="py-line"> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">"__main__"</tt><tt class="py-op">:</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line">    <tt class="py-keyword">print</tt> <tt class="py-string">"Hello World"</tt><tt class="py-op">;</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line"> </tt><script type="text/javascript">
<!--
expandto(location.href);
// -->
</script>
</pre>
<br />
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
       bgcolor="#a0c0ff" cellspacing="0">
  <tr valign="middle">
  <!-- Home link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="BIP-module.html">Home</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Tree link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Index link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Help link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Project homepage -->
      <th class="navbar" align="right" width="100%">
        <table border="0" cellpadding="0" cellspacing="0">
          <tr><th class="navbar" align="center"
            ><a class="navbar" target="_top" href="http://code.google.com/p/bayesian-inference">Project Homepage</a></th>
          </tr></table></th>
  </tr>
</table>
<table border="0" cellpadding="0" cellspacing="0" width="100%%">
  <tr>
    <td align="left" class="footer">
    Generated by Epydoc 3.0.1 on Thu Jan  7 10:45:34 2010
    </td>
    <td align="right" class="footer">
      <a target="mainFrame" href="http://epydoc.sourceforge.net"
        >http://epydoc.sourceforge.net</a>
    </td>
  </tr>
</table>

<script type="text/javascript">
  <!--
  // Private objects are initially displayed (because if
  // javascript is turned off then we want them to be
  // visible); but by default, we want to hide them.  So hide
  // them unless we have a cookie that says to show them.
  checkCookie();
  // -->
</script>
</body>
</html>
